Nickel in PDB 3uyj: Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg

All present enzymatic activity of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg:
1.14.11.27;

The structure of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg, PDB code: 3uyj was solved by X.Su, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.35
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.393, 68.393, 266.686, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 25.3

The binding sites of Nickel atom in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg (pdb code 3uyj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg, PDB code: 3uyj:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:36.7 occ:1.00 OD2 A:ASP323 1.9 38.7 1.0 O1 A:AKG601 1.9 36.8 1.0 NE2 A:HIS321 2.0 34.1 1.0 O5 A:AKG601 2.1 36.6 1.0 NE2 A:HIS400 2.2 38.3 1.0 O A:HOH5 2.3 39.2 1.0 C1 A:AKG601 2.7 37.4 1.0 C2 A:AKG601 2.7 34.5 1.0 CG A:ASP323 3.0 39.7 1.0 CD2 A:HIS321 3.0 36.0 1.0 CE1 A:HIS321 3.0 38.2 1.0 CD2 A:HIS400 3.2 35.2 1.0 CE1 A:HIS400 3.2 39.8 1.0 OD1 A:ASP323 3.3 44.9 1.0 O A:HOH58 3.8 36.9 1.0 O2 A:AKG601 3.9 35.8 1.0 ND1 A:HIS321 4.1 35.6 1.0 CG A:HIS321 4.1 35.5 1.0 O A:HOH66 4.1 46.2 1.0 C3 A:AKG601 4.2 35.8 1.0 ND1 A:HIS400 4.3 40.8 1.0 CG A:HIS400 4.3 34.8 1.0 CB A:ASP323 4.4 34.3 1.0 CZ2 A:TRP414 4.6 36.9 1.0 H32 A:AKG601 4.6 43.0 1.0 H41 A:AKG601 4.7 39.8 1.0 H31 A:AKG601 4.7 43.0 1.0 H42 A:AKG601 4.8 39.8 1.0 C4 A:AKG601 4.8 33.2 1.0 ND2 A:ASN327 5.0 34.1 1.0 NE1 A:TRP414 5.0 41.2 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:40.4 occ:1.00 NE2 B:HIS321 2.0 44.8 1.0 OD2 B:ASP323 2.1 42.9 1.0 O5 B:AKG601 2.1 43.4 1.0 O1 B:AKG601 2.1 39.7 1.0 NE2 B:HIS400 2.2 45.5 1.0 O B:HOH19 2.3 37.6 1.0 C2 B:AKG601 2.8 36.9 1.0 C1 B:AKG601 2.8 38.0 1.0 CD2 B:HIS321 3.0 42.4 1.0 CE1 B:HIS321 3.0 44.5 1.0 CG B:ASP323 3.0 41.3 1.0 CE1 B:HIS400 3.2 39.4 1.0 OD1 B:ASP323 3.2 43.6 1.0 CD2 B:HIS400 3.3 45.2 1.0 O2 B:AKG601 4.0 41.1 1.0 ND1 B:HIS321 4.1 44.9 1.0 CG B:HIS321 4.1 43.2 1.0 C3 B:AKG601 4.2 38.3 1.0 O B:HOH124 4.3 49.4 1.0 ND1 B:HIS400 4.3 41.9 1.0 CG B:HIS400 4.4 45.7 1.0 CB B:ASP323 4.4 37.6 1.0 CZ2 B:TRP414 4.6 39.8 1.0 H32 B:AKG601 4.6 46.0 1.0 H41 B:AKG601 4.6 45.7 1.0 H42 B:AKG601 4.8 45.7 1.0 H31 B:AKG601 4.8 46.0 1.0 C4 B:AKG601 4.8 38.1 1.0 NE1 B:TRP414 4.9 41.3 1.0 ND2 B:ASN327 5.0 34.5 1.0

X.Su, H.Li. Crystal Structure of JMJD5 Catalytic Core Domain in Complex with Nickle and Alpha-Kg To Be Published.